DNA Hydrogel Research Articles

Kloramfenikol Aptameri Fonksiyonlandırılmış DNA Hidrojellerinin Sentez Koşullarının Optimizasyonu

Aptamer fonksiyonlandırılmış DNA hidrojelleri yüksek özgünlük, stabilite ve esneklik gibi özellikleri nedeniyle birçok alanda kullanılmaktadır. Bu çalışma kapsamında kloramfenikole özgü aptamer dizisi fonksiyonlandırılmış DNA hidrojeli sentezi gerçekleştirilmiş ve hidrojel stabilitesi için önemli parametreler optimize edilmiştir. Sentez için 5’ uçları akridit modifiyeli kloramfenikole özgü aptamer ile ona kısmen eşlenik DNA ipliği polimer yapıya yan dal olarak katılmış ve eşlenik bölgelerin hibridizasyonu ile bir arada tutularak hidrojel sentezi gerçekleştirilmiştir. Optimize edilmiş parametreler akridit modifiyeli DNA dizilerinin konsantrasyonları, akrilamid yüzdesi, kloramfenikol aptameri ve DNA iplik 1 içeren lineer polimer çözeltilerin molar oranlarıdır. Ayrıca, reaksiyon sıcaklığı ve eşlenik bölgenin uzunluğunun jel stabilitesine etkisi değerlendirilmiştir. Sonuç olarak, DNA hidrojel stabilitesi için %60’lık lineer poliakrilamid-DNA konjugasyonundan, %40 akrilamid stok çözeltisi kullanılarak 1:1 molar oranda karıştırılan aptamer ve DNA iplik çözeltileri ile 25°C’de aptamer fonksiyonlandırılmış DNA hidrojeli sentezi tamamlanmıştır. Bunlara ek olarak, aptamer dizisi ile DNA iplik arasındaki eşlenik bölgenin uzunluğunun stabiliteyi artırdığı sonucuna varılmıştır.

In situ generated PANI promoted flexible photoelectrochemical biosensor for ochratoxin A based on GOx-stuffed DNA hydrogel as enhancer

Aflexible photoelectrochemical (PEC) biosensor isproposed for the sensitive detection of ochratoxin A (OTA) based on glucose oxidase (GOx)-encapsulated target-responsive hydrogel, using Fenton reaction-mediated in situ formation of polyaniline (PANI) as signal amplified strategy. The target-responsive DNA hydrogels with high loading capacity can carry a large amount of GOx, which not only avoids laborious labeling process but also enhances the analytical performance. Upon introduction of target molecules, the hydrogel can be opened, and multiple GOx was released, thus producing lots of H2O2 via catalytic reduction of glucose. As a component of the Fenton reagent, H2O2 can react with the Fe2+ on the graphene oxidase-PAMAM-Fe2+ (GO-PAMAM-Fe2+) to generate Fe3+ and ·OH. This in turn can oxidize aniline and generate polyaniline (PANI), resulting in the enhancement of the photocurrent signal of GO-MoS2-CdS photoelectrode. The GO-PAMAM-Fe2+ as the neighborhood component of GO-MoS2-CdS-based photoactive material not only can increase the loading amount of Fe2+, but also can inhibit the decrease of photocurrent of GO-MoS2-CdS by direct modification of Fe2+ on the photoactive material. Moreover, the high loading capacity of DNA hydrogel can efficiently promote the performance of the PEC biosensor. The PEC biosensor exhibited satisfactory analytical performance for OTA with a linear range of 0.0001-0.1ng/mL and a low detection limit of 0.05pg/mL. Itpresents recommendable specificity, stability, and practical applications. Importantly, the PEC biosensor provides a new concept for construction of PEC biosensing platform.

Self‐Mineralizing Dnazyme Hydrogel as a Multifaceted Bone Microenvironment Amendment for Promoting Osteogenesis in Osteoporosis

AbstractThe accumulation of reactive oxygen species (ROS) and minimal osteogenic raw material in the osteoporotic bone microenvironment greatly inhibits the activity of osteoblasts. Herein, it is originally proposed to construct a biomatrix multifaceted bone microenvironment amendment ‐Mineralized zippered G4‐Hemin DNAzyme hydrogel (MDH)‐to improve osteoporotic osteogenic capacity and promote high‐quality bone defect repair. The programmed design of the rolling circle amplified DNA hydrogel synthesis system allows the introduction of massive amounts of zippered G4‐Hemin DNAzyme in MDH. The zippered G4‐Hemin DNAzyme highly mimics the tight catalytic configuration of horseradish peroxidase and exerts excellent enzyme‐like activity with considerable ROS molecule scavenging ability. In addition, the DNA amplification by‐product pyrophosphate is ingeniously employed as a sufficient phosphorus source, thus constituting an autonomous mineralization system for waste reuse through the introduction of pyrophosphate hydrolase and calcium ions, which deposits in MDH as an osteogenic raw material and addresses the challenge of DNA hydrogel bio‐application stability. The remarkable in vitro and in vivo outcomes demonstrate that MDH can effectively improve the oxidative stress status of osteoblasts, restore the balance of mitochondrial membrane potential, and reduce apoptosis, ultimately demonstrating superior osteogenic capacity.

Stimulus-Responsive DNA Hydrogel Biosensors for Food Safety Detection.

Food safety has always been a major global challenge to human health and the effective detection of harmful substances in food can reduce the risk to human health. However, the food industry has been plagued by a lack of effective and sensitive safety monitoring methods due to the tension between the cost and effectiveness of monitoring. DNA-based hydrogels combine the advantages of biocompatibility, programmability, the molecular recognition of DNA molecules, and the hydrophilicity of hydrogels, making them a hotspot in the research field of new nanomaterials. The stimulus response property greatly broadens the function and application range of DNA hydrogel. In recent years, DNA hydrogels based on stimulus-responsive mechanisms have been widely applied in the field of biosensing for the detection of a variety of target substances, including various food contaminants. In this review, we describe the recent advances in the preparation of stimuli-responsive DNA hydrogels, highlighting the progress of its application in food safety detection. Finally, we also discuss the challenges and future application of stimulus-responsive DNA hydrogels.

Stimuli-Responsive Self-Degradable DNA Hydrogels: Design, Synthesis, and Applications.

DNA hydrogels play an increasingly important role in biomedicine and bioanalysis applications. Due to their high programmability, multifunctionality and biocompatibility, they are often used as effective carriers for packing drugs, cells, or other bioactive cargoes in vitro and in vivo. However, the stability of the DNA hydrogels prevents their in-demand rapid release of cargoes to achieve a full therapeutic effect in time. For bioanalysis, the generation of signals sometimes needs the DNA hydrogel to be rapidly degraded when sensing target molecules. To meet these requirements, stimulus-responsive DNA hydrogels are designed. By responding to different stimuli, self-degradable DNA hydrogels can switch from gel to solution for quantitative bioanalysis and precision cargo delivery. This review summarizes the recently developed innovative methods for designing stimuli-responsive self-degradable DNA hydrogels and showed their applications in the bioanalysis and biomedicines fields. Challenges, as well as prospects, are also discussed.

The development of a paper-based distance sensor for the detection of Pb2+ assisted with the target-responsive DNA hydrogel

Due to the serious risks of lead pollution to human health, it plays a great role in constructing a simple, inexpensive, portable, and user-friendly strategy for Pb2+ detection in environmental samples. Herein, a paper-based distance sensor is developed to detect Pb2+ assisted with the target-responsive DNA hydrogel. Pb2+ can activate DNAzyme to cleave its substrate strand, which results in the hydrolysis of the DNA hydrogel. The released water molecules trapped in the hydrogel can flow along the patterned pH paper due to the capillary force. The water flow distance (WFD) is significantly influenced by the amount of water released from the collapsed DNA hydrogel triggered by the addition of various Pb2+ concentrations. In this way, Pb2+ can be quantitatively detected without using specialized instruments and labeled molecules, and the limit of detection (LOD) of Pb2+ is 3.0 nM. Additionally, the Pb2+ sensor works well in lake water and tap water. Overall, this simple, inexpensive, portable, and user-friendly method is very promising for quantitative and in-field detection of Pb2+ with excellent sensitivity and selectivity.

Frontispiece: Assembly of Rolling Circle Amplification‐Produced Ultralong Single‐Stranded DNA to Construct Biofunctional DNA Materials

Recent developments in biofunctional DNA hydrogels and DNA nanocomplexes based on rolling circle amplification (RCA) are described and assembly strategies and functionalization methods of the ultralong single-strand DNA produced by RCA to construct biofunctional materials are introduced in the Review article by Yang, Yao et al. (DOI: 10.1002/chem.202202673).

Colorimetric aptasensor for fumonisin B1 detection based on the DNA tetrahedra-functionalized magnetic beads and DNA hydrogel-coated bimetallic MOFzyme.

The toxicity and incidence of fumonisin B1 (FB1) pose a major challenge to public health and the environment, prompting the development of alternative quantitative strategies for FB1. Herein, a colorimetric aptasensor was constructed based on DNA tetrahedra-functionalized magnetic beads (MBs) and DNA hydrogel-coated Mn-Zr bimetallic metal-organic frameworks-based nanozyme (MOFzyme). Initially, MBs functionalized by DNA tetrahedra demonstrated excellent capturing capability for FB1. Along with the capture of FB1, catalyst DNA (C) was released into the supernatant. Aided by fuel DNA (F), C can trigger continuous cleavage of the main chains and cross-linking points of the DNA hydrogel through an entropy-driven DNA circuit integrated into the hydrogel coating. Subsequently, the bimetallic MOFzyme encapsulated inside the DNA hydrogel was exposed and exerted its superb peroxidase-like activity, producing a colorimetric signal whose intensity was positively dependent on the amount of FB1. The developed aptasensor exhibited good linearity in the range of 5×10-4 to 50ngmL-1 with a limit of detection (LOD) of 0.38pgmL-1, and reasonable specificity in different matrices. Furthermore, the aptasensor was successfully applied to quantify FB1 in actual samples with recoveries fell within 92.25 %-108.00 %, showing its great potential in environmental monitoring and food safety.

Intradermal delivery of Cryj1 loaded in CpG DNA hydrogel for inhibiting allergic reactions in mice.

Immunotherapy for allergic rhinitis alleviates symptoms associated with antigen exposure by administering pathogenic antigens. However, many current immunotherapies fail to induce sufficient immune responses, resulting in frequent and prolonged hospital visits. Consequently, the development of more effective immunotherapies is necessary. In this study, we focused on the skin, which is rich in immune cells, as an administration site for inducing antigen-specific immune responses. To efficiently and sustainably deliver the cedar pollen antigen Cryj1 to immune cells, we attempted to load Cryj1 in an immunostimulatory CpG DNA hydrogel, prepared using self-gelatinizable nucleic acid technology. In this technology, the hydrogel became gelatinized by self-assembly of multiple predesigned DNA units containing potent CpG motifs. Cryj1 loaded in the CpG DNA hydrogel showed sustained release, was taken up by mouse macrophage-like RAW264.7 and mouse dendritic DC2.4 cells, and induced efficient production of interleukin-12 after intradermal injection into mice. Intradermal injection of Cryj1 loaded CpG DNA hydrogel into mice increased the production of Cryj1-specific IgG while suppressing the production of immunoglobulin E (IgE) antibodies. Furthermore, when Cryj1 was resensitized to mice, a stronger induction of IgG production and suppression of IgE production was observed. These results suggest that intradermal administration of Cryj1 loaded CpG DNA hydrogel is a novel immunotherapy for allergic symptoms caused by cedar pollen and can be used as a replacement for current immunotherapies.

Bimetallic nanozymes laden DNA hydrogel for ultrasensitive optical detection of ractopamine

Ractopamine (RAC) is a synthetic β-adrenergic agonist, used for the reduction of fat deposition and increasing muscle conversion. Despite its wide application as a feed additive, it has some serious side effects. Therefore, RAC exists at low concentrations in meat products and is difficult to detect, hence its ultrasensitive detection is significant in protecting human health. Herein, a novel nanozymes-laden bioactive hydrogel based on the Au@Pd and DNA hydrogel is developed for ultrasensitive optical detection of RAC. The RAC aptamer acts as a crosslinker and Au@Pd is evenly embedded in the DNA hydrogel. The formed hydrogel collapses when the RAC binds to the aptamer, releasing the embedded Au@Pd. This catalyst is then used in the reaction of hydrogen peroxide (H2O2) with tetramethyl benzidine (TMB) to produce color changes that deepen with increasing RAC concentration. The proposed nanozymes-laden bioactive hydrogel has a low detection limit (7.39 ng L−1) and a wide detection range (0.01–1000 μg L−1) and is of great potential for future practical applications in the ultrasensitive detection of food additives.

An Update of DNA Hydrogel Application in Biosensing

AbstractDNA gel not only uses the skeleton function of hydrogel but also the biological function of DNA to realize the unified fusion of the structure and function of hydrogel material. By introducing specific small molecules into the DNA gel, it can respond to pH, temperature, ultraviolet, infrared, metal ions, and drug small molecules. To further realize the detection and loading of various small molecules in the biomedical field, the specific recognition and detection of heavy metal ions and toxins in the environment are done. In this paper, the preparation of pure DNA gel and hybrid DNA gel, their detection in the biomedical and environmental fields are reviewed, and their prospects and further development directions are discussed.

A Strong Acid-Induced DNA Hydrogel Based on pH-Reconfigurable A-Motif Duplex.

Under a pH value lower than the pKa of adenine (3.5), adenine-rich sequences (A-strand) form a unique parallel A-motif duplex due to the protonation of A-strand. At a pH above 3.5, deprotonation of adenines leads to the dissolution of A-motif duplex to A-strand single coil. This pH-reconfigurable A-motif duplex has been developed as a novel pH-responsive DNA hydrogel, termed A-hydrogel. The hydrogel state is achieved at pH 1.2 by the A-motif duplex bridging units, which are cross-linked by both reverse Hoogsteen interaction and electrostatic attraction. Hydrogel-to-solution transition is triggered by pH 4.3 due to the deprotonation-induced separation of A-motif duplex. The A-hydrogel system undergoes reversible hydrogel-solution transitions by subjecting the system to cyclic pH shifts between 1.2 and 4.3. An anti-inflammatory medicine, sulfasalazine (SSZ), which intercalates into A-motif duplex, is loaded into A-hydrogel. Its pH-controlled release from A-hydrogel is successfully demonstrated. The strong acid-induced A-hydrogel may fill the gap that other mild acid-responsive DNA hydrogels cannot do, such as protection of orally delivered drug in hostile stomach environment against strong acid (pH ~ 1.2) and digestive enzymes.

Nucleic acid-based artificial nanocarriers for gene therapy.

Nucleic acid nanotechnology is a powerful tool in the fields of biosensing and nanomedicine owing to their high editability and easy synthesis and modification. Artificial nucleic acid nanostructures have become an emerging research hotspot as gene carriers with low cytotoxicity and immunogenicity for therapeutic approaches. In this review, recent progress in the design and functional mechanisms of nucleic acid-based artificial nano-vectors especially for exogenous siRNA and antisense oligonucleotide delivery is summarized. Different types of DNA nanocarriers, including DNA junctions, tetrahedrons, origami, hydrogels and scaffolds, are introduced. The enhanced targeting strategies to improve the delivery efficacy are demonstrated. Furthermore, RNA based gene nanocarrier systems by self-assembly of short strands, rolling circle transcription, chemical crosslinking and using RNA motifs and DNA-RNA hybrids are demonstrated. Finally, the outlook and potential challenges are highlighted. The nucleic acid-based artificial nanocarriers offer a promising and precise tool for gene delivery and therapy.

RNA-DNA hybrid nano-materials for highly efficient and long lasting RNA interference effect.

In attempts to effectively improve RNAi function, we herein report a new RNAi approach using X-shaped RDNA and Dgel (RNA interfering DNA hydrogel, Ri-Dgel). X-shaped RDNA is a 4 branched nanostructure which was composed of three dsDNA branches and one dsRNA branch, and the structure was made by annealing partially complementary ssDNAs and chimeric RNA-DNA oligonucleotides. Ri-Dgel was synthesized through the ligation of the X-shaped RDNAs using their palindromic sticky ends. In MDCK/GFP cells transfected with 1 μM of each format of siRNA, Ri-Dgel and X-RDNA, the intensity of GFP fluorescence was significantly reduced by 65% and 56%, respectively, while dsRNA which is a conventional siRNA format showed a relatively weak reduction intensity of 7% compared with a negative control. We also observed the decreased intensity of GFP fluorescence by approximately 59% in MDA-MB-231/GFP cells transfected with 5 nM Ri-Dgel. Furthermore, the Ri-Dgel showed persistent RNAi efficiency up to 6 days from the treatment. The use of Ri-Dgel to trigger RNAi resulted in enhanced efficacy and longer duration at lower concentration compared to traditional dsRNA implying the nanostructured DNA-RNA hybrid materials have great potential as a platform technology for RNAi-based therapy.

Nanostars planarity modulates the rheology of DNA hydrogels.

In analogy with classic rigidity problems of networks and frames, the elastic properties of hydrogels made of DNA nanostars (DNAns) are expected to strongly depend on the precise geometry of their building blocks. However, it is currently not possible to determine DNAns shape experimentally. Computational coarse-grained models that can retain the correct geometry of DNA nanostars and account for the bulk properties observed in recent experiments could provide missing insights. In this study, we perform metadynamics simulations to obtain the preferred configuration of three-armed DNA nanostars simulated with the oxDNA model. Based on these results we introduce a coarse-grained computational model of nanostars that can self assemble into complex three dimensional percolating networks. We compare two systems with different designs, in which either planar or non-planar nanostars are used. Structural and network analysis reveal completely different features for the two cases, leading to two contrasting rheological properties. The mobility of molecules is larger in the non-planar case, which is consistent with a lower viscosity measured from Green-Kubo simulations in equilibrium. To the best of our knowledge, this is the first work connecting the geometry of DNAns with the bulk rheological properties of DNA hydrogels and may inform the design of future DNA based materials.

A portable and partitioned DNA hydrogel chip for multitarget detection.

A DNA hydrogel, owing to its dual properties of liquid and solid, is considered to be an ideal material for constructing biosensors that can integrate the advantages of both wet chemistry and dry chemistry. Nevertheless, it has struggled to cope with the demands of high-throughput analysis. A partitioned and chip-based DNA hydrogel is a potential avenue to achieve this, but currently remains a formidable challenge. Here, we developed a portable and partitioned DNA hydrogel chip that can be used for multitarget detection. The partitioned and surface-immobilized DNA hydrogel chip was formed by inter-crosslinking amplification by incorporating target-recognizing fluorescent aptamer hairpins into multiple rolling circle amplification products, which can achieve portable and simultaneous detection of multiple targets. This approach expands the application of semi-dry chemistry strategies, which can realize high throughput and point of care testing (POCT) of different targets, improving the development of hydrogel-based bioanalysis and providing new potential solutions for biomedical detection.

Accurate quantification of DNA content in DNA hydrogels prepared by rolling circle amplification.

Accurate quantification of polymerized DNA in rolling circle amplification (RCA)-based hydrogels is challenging due to the high viscosity of these materials, however, it can be achieved with a photometric nucleotide depletion assay or qPCR. We show that the DNA content strongly depends on the template sequence and correlates with the mechanical properties of the hydrogels.

Potential mechanism of the AgNCs-hydrogel in promoting the regeneration of diabetic infectious wounds.

Diabetic infectious wound treatment is challenging due to insistent wound infections. To treat such complicated pathological diabetic infectious wounds, multifunctional materials need to be developed, and their mechanisms need to be understood. Here, we developed a material termed AgNCs-hydrogel, which is a multifunctional DNA hydrogel used as dressings by integrating it with antibacterial silver nanoclusters. The AgNCs-hydrogel was applied to promote the regeneration of diabetic infectious wounds in mice because it exhibited superior antibacterial activity and effective ROS-scavenging properties. Based on skin proteomics, we explored the potential mechanism of the AgNCs-hydrogel in treating mouse skin wounds. We found that the AgNCs-hydrogel can regulate some key proteins located primarily in the extracellular exosomes, involved in the negative regulation of the apoptotic process, and perform ATP binding to accelerate diabetic infected wound closure. Therefore, this study provided a multifunctional AgNCs-hydrogel and revealed its potential mechanism in promoting the regeneration of diabetic infectious wounds.

Tuning Plasmonic Properties of Gold Nanoparticles by Employing Nanoscale DNA Hydrogel Scaffolds

Noble metals have always fascinated researchers due to their feasible and facile approach to plasmonics. Especially the extensive utilization of gold (Au) has been found in biomedical engineering, microelectronics, and catalysis. Surface plasmonic resonance (SPR) sensors are achievable by employing plasmonic nanoparticles. The past decades have seen colossal advancement in noble metal nanoparticle research. Surface plasmonic biosensors are advanced in terms of sensing accuracy and detection limit. Likewise, gold nanoparticles (AuNPs) have been widely used to develop distinct biosensors for molecular diagnosis. DNA nanotechnology facilitates advanced nanostructure having unique properties that contribute vastly to clinical therapeutics. The critical element for absolute control of materials at the nanoscale is the engineering of optical and plasmonic characteristics of the polymeric and metallic nanostructure. Correspondingly, AuNP's vivid intense color expressions are dependent on their size, shape, and compositions, which implies their strong influence on tuning the plasmonic properties. These plasmonic properties of AuNPs have vastly exerted the biosensing and molecular diagnosis applications without any hazardous effects. Here, we have designed nanoscale X-DNA-based Dgel scaffolds utilized for tuning the plasmonic properties of AuNPs. The DNA nanohydrogel (Dgel) scaffolds engineered with three different X-DNAs of distinct numbers of base pairs were applied. We have designed X-DNA base pair-controlled size-varied Dgel scaffolds and molar ratio-based nano assemblies to tune the plasmonic properties of AuNPs. The nanoscale DNA hydrogel's negatively charged scaffold facilitates quaternary ammonium ligand-modified positively charged AuNPs to flocculate around due to electrostatic charge attractions. Overall, our study demonstrates that by altering the DNA hydrogel scaffolds and the physical properties of the nanoscale hydrogel matrix, the SPR properties can be modulated. This approach could potentially benefit in monitoring diverse therapeutic biomolecules.

Assembly of Rolling Circle Amplification-Produced Ultralong Single-Stranded DNA to Construct Biofunctional DNA Materials.

The Review by Yang, Yao and colleagues (DOI: 10.1002/chem.202202673) describes recent developments in biofunctional DNA hydrogels and DNA nanocomplexes based on rolling circle amplification (RCA) and introduces assembly strategies and functionalization methods of the ultralong single-strand DNA produced by RCA to construct biofunctional materials.